I have a set of annotations (pasted below). When I use the goSlim function in order to have the counts of appearance of each Go Slim plant ontology, it seems to me that the counts are off.

I noticed it because I am interested in one perticular ontology which is "GO:0005618" (cell wall), appearing two times in my annotation file but which is counted only one. Is there something I am missing here?

Sorry for my slow response, but yes, this seems to be a bug; thanks! It is fixed in version 1.38.2, which should become available via biocLite() on Thursday after about 2pm Eastern, all being well. The updated output is

with increments occurring both in the primary id and also offspring. For instance the count for GO:0005575 changes from 4 to 6 because it is represented twice as primary id, twice as child of the duplicated id GO0005618, and once each as child of the unique ids GO:0005576 and 0005886.